• Journal of Microbiology and Biotechnology
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• v.22 no.1
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• pp.46-49
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• 2012

The Vibrio vulnificus vuuA gene, of which expression is repressed by a complex of iron and ferric uptake regulator (Fur), was characterized to localize the Fur-binding site in its upstream regulatory region. In silico analysis suggested the presence of two possible Fur-binding sites; one is a classical Fur-box and the other is a previously reported distinct Fur-binding site. Site-directed mutagenesis and DNase I protection assays revealed the binding site for the iron-Fur complex, which includes an extended inverted repeat containing a homologous sequence to the classical Fur-box.

• Journal of Integrative Natural Science
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• v.16 no.2
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• pp.53-59
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• 2023

Lavender oil is a prolonged history in ancient medicine and has a wide range of biological effects. The lavender essential oil has 50 different constituents that have different therapeutic significance. The compounds that are separated from essential oil can be used for the anticancer treatment of non-small cell lung cancer. ROS1 is one of the major targets for NSCLC. The compounds from lavender essential oil are separated through GC-MS. From 91 compounds the top compounds that are having high retention values are taken for Molecular docking study against the ROS1 target protein. The binding affinity and the docked pose for those compounds are studied. Later, the chemical reactivity of the compounds is studied by Density Functional Theory. The potent compounds must be validated by in vivo study.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.11 no.2
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• pp.720-726
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• 2010

Haplotype-based research has become increasingly important in the field of personalized medicine since the haplotype reflects a set of SNPs (Single Nucleotide Polymorphisms) that are genetically associated and inherited together. Currently, the most widely used application softwares available for haplotype reconstruction, based on in silico method, include PL-EM, Haplotyper, PHASE and HAP. PL-EM, Haplotyper and PHASE are command-line application running on LINUX or Unix system and HAP is a web-based client-server application. This paper deals with an integrated haplotype reconstruction system that have been developed with PL-EM and Haplotyper selected from the accuracy test with experimentally verified data on public application softwares. This integrated system is a kind of client-sever one with user friendly web interface and can provide end-users with a high quality of haplotype analysis. SNPs genotype data with a length of 5 derived from 5 people and SNPs genotype data with a length of 13 derived from 15 people were used to test the analysis results of Haplotyper and PL-EM respectively. As a result, this system has been confirmed to provide the systematic and easy-to-understand analysis results that consist of two main parts, i.e. individual haplotype information and haplotype pool information. In this respect, the integration system will be utilized as a useful tool for the discovery of disease related genes and the development of personalized drugs through facilitating the reconstruction of haplotype maps.

• Journal of Life Science
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• v.19 no.8
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• pp.1159-1163
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• 2009

It has been postulated that endoplasmic (ER) stress is involved in the development of several diseases. However, the detailed molecular mechanisms have not been fully understood. Therefore, we characterized a genetic network of genes induced by ER stress using cDNA microarray and gene set expression coherence analysis (GSECA), and identified gene function as well as several transcription regulators associated with ER stress. We analyzed time-dependent gene expression profiles in thapsigargin-treated Sk-Hep1 using an oligonucleotide expression chip, and then selected functional gene sets with significantly high expression coherence which was processed into functional clusters according to the expression similarities. The functions related to sugar binding, lysosome, ribosomal protein, ER lumen, and ER to golgi transport increased, whereas the functions with mRNA processing, DNA replication, DNA repair, cell cycle, electron transport chain and helicase activity decreased. Furthermore, functional clusters were investigated for the enrichment of regulatory motifs using GSECA, and several transcriptional regulators associated with regulation of ER-induced gene expression were found.

• The Plant Pathology Journal
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• v.36 no.5
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• pp.491-496
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• 2020

An understanding of the contribution of secondary metabolites (SMs) to the antagonistic and biocontrol activities of bacterial biocontrol agents serves to improve biocontrol potential of the strain. In this study, to evaluate the contribution of each SM produced by Pseudomonas fluorescens NBC275 (Pf275) to its antifungal and biocontrol activity, we combined in silico analysis of the genome with our previous study of transposon (Tn) mutants. Thirteen Tn mutants, which belonged to 6 biosynthetic gene clusters (BGCs) of a total 14 BGCs predicted by the antiSMASH tool were identified by the reduction of antifungal activity. The biocontrol performance of Pf275 was significantly dependent on 2,4-diacetylphloroglucinol and pyoverdine. The clusters that encode for arylpolyene and an unidentified small linear lipopeptide influenced antifungal and biocontrol activities. To our knowledge, our study identified the contribution of SMs, such as a small linear lipopeptide and arylpolyene, to biocontrol efficacy for the first time.

• 한국생물공학회:학술대회논문집
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• 2005.10a
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• pp.634-634
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• 2005

• Journal of Animal Science and Technology
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• v.63 no.6
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• pp.1468-1472
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• 2021

Clostridium perfringens B20 was isolated from chicken feces collected from a local farm associated with Chung-Ang University (Anseong, Korea). The whole genome of C. perfringens B20 was sequenced using the PacBio RS II platform and assembled de novo. The genome is 2,982,563 bp long and assembled in two contigs. Annotation analyses revealed 2,668 protein-coding sequences, 30 rRNA genes, and 94 tRNA genes, with 28.2% G + C (guanine + cytosine) content. In silico genomic analysis revealed the presence of genes encoding a class IId bacteriocin, lactococcin A, and associated ABC transporter and immunity proteins, as well as a putative bacteriocin gene.

• Genomics & Informatics
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• v.12 no.2
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• pp.64-70
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• 2014

Human papillomavirus (HPV) infection is the leading cause of cancer mortality among women worldwide. The life-threatening infection caused by HPV demands the need for designing anticancerous drugs. In the recent years, different compounds from natural origins, such as carrageenan, curcumin, epigallocatechin gallate, indole-3-carbinol, jaceosidin, and withaferin, have been used as a hopeful source of anticancer therapy. These compounds have been shown to suppress HPV infection by different researchers. In the present study, we explored these natural inhibitors against E6 oncoprotein of high-risk HPV-16, which is known to inactivate the p53 tumor suppressor protein. A robust homology model of HPV-16 E6 was built to anticipate the interaction mechanism of E6 oncoprotein with natural inhibitory molecules using a structure-based drug designing approach. Docking analysis showed the interaction of these natural compounds with the p53-binding site of E6 protein residues 113-122 (CQKPLCPEEK) and helped the restoration of p53 functioning. Docking analysis, besides helping in silico validation of natural compounds, also helps understand molecular mechanisms of protein-ligand interactions.

• Genomics & Informatics
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• v.21 no.3
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• pp.41.1-41.11
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• 2023

The Dengue virus M protein is a 75 amino acid polypeptide with two helical transmembranes (TM). The TM domain oligomerizes to form an ion channel, facilitating viral release from the host cells. The M protein has a critical role in the virus entry and life cycle, making it a potent drug target. The oligomerization of the monomeric protein was studied using ab initio modeling and molecular dynamics simulation in an implicit membrane environment. The representative structures obtained showed pentamer as the most stable oligomeric state, resembling an ion channel. Glutamic acid, threonine, serine, tryptophan, alanine, isoleucine form the pore-lining residues of the pentameric channel, conferring an overall negative charge to the channel with approximate length of 51.9 Å. Residue interaction analysis for M protein shows that Ala94, Leu95, Ser112, Glu124, and Phe155 are the central hub residues representing the physicochemical interactions between domains. The virtual screening with 165 different ion channel inhibitors from the ion channel library shows monovalent ion channel blockers, namely lumacaftor, glipizide, gliquidone, glisoxepide, and azelnidipine to be the inhibitors with high docking scores. Understanding the three-dimensional structure of M protein will help design therapeutics and vaccines for Dengue infection.

• 한국생물공학회:학술대회논문집
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• 2005.10a
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• pp.586-587
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• 2005